--- _id: '429' abstract: - lang: eng text: We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent. acknowledgement: "Open access funding provided by Institute of Science and Technology (IST Austria).\r\n" article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Oskari H full_name: Ajanki, Oskari H id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87 last_name: Ajanki - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373. doi:10.1007/s00440-018-0835-z apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z. ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” Probability Theory and Related Fields, vol. 173, no. 1–2. Springer, pp. 293–373, 2019. ista: Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373. mla: Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z. short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373. date_created: 2018-12-11T11:46:25Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-08-24T14:39:00Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00440-018-0835-z ec_funded: 1 external_id: isi: - '000459396500007' file: - access_level: open_access checksum: f9354fa5c71f9edd17132588f0dc7d01 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:12:08Z date_updated: 2020-07-14T12:46:26Z file_id: '5720' file_name: 2018_ProbTheory_Ajanki.pdf file_size: 1201840 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 173' isi: 1 issue: 1-2 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 293–373 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Probability Theory and Related Fields publication_identifier: eissn: - '14322064' issn: - '01788051' publication_status: published publisher: Springer publist_id: '7394' quality_controlled: '1' scopus_import: '1' status: public title: Stability of the matrix Dyson equation and random matrices with correlations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 173 year: '2019' ... --- _id: '5947' abstract: - lang: eng text: Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking. article_processing_charge: No author: - first_name: Bapi full_name: Chatterjee, Bapi id: 3C41A08A-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-2742-4028 - first_name: Sathya full_name: Peri, Sathya last_name: Peri - first_name: Muktikanta full_name: Sa, Muktikanta last_name: Sa - first_name: Nandini full_name: Singhal, Nandini last_name: Singhal citation: ama: 'Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: ACM International Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617' apa: 'Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In ACM International Conference Proceeding Series (pp. 168–177). Bangalore, India: ACM. https://doi.org/10.1145/3288599.3288617' chicago: Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In ACM International Conference Proceeding Series, 168–77. ACM, 2019. https://doi.org/10.1145/3288599.3288617. ieee: B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in ACM International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177. ista: 'Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.' mla: Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” ACM International Conference Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617. short: B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177. conference: end_date: 2019-01-07 location: Bangalore, India name: 'ICDCN: Conference on Distributed Computing and Networking' start_date: 2019-01-04 date_created: 2019-02-10T22:59:17Z date_published: 2019-01-04T00:00:00Z date_updated: 2023-08-24T14:41:53Z day: '04' department: - _id: DaAl doi: 10.1145/3288599.3288617 external_id: arxiv: - '1809.00896' isi: - '000484491600019' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.00896 month: '01' oa: 1 oa_version: Preprint page: 168-177 publication: ACM International Conference Proceeding Series publication_identifier: isbn: - '978-1-4503-6094-4 ' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '5857' abstract: - lang: eng text: 'A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n.' article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: János full_name: Pach, János last_name: Pach citation: ama: 'Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics. 2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025' apa: 'Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025' chicago: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.' ieee: 'R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.' ista: 'Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231.' mla: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.' short: R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231. date_created: 2019-01-20T22:59:17Z date_published: 2019-04-30T00:00:00Z date_updated: 2023-08-24T14:39:33Z day: '30' department: - _id: UlWa doi: 10.1016/j.dam.2018.12.025 external_id: arxiv: - '1708.08037' isi: - '000466061100020' intvolume: ' 259' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.08037 month: '04' oa: 1 oa_version: Preprint page: 266-231 project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: Discrete Applied Mathematics publication_identifier: issn: - 0166218X publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '433' relation: earlier_version status: public scopus_import: '1' status: public title: 'Thrackles: An improved upper bound' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 259 year: '2019' ... --- _id: '5944' abstract: - lang: eng text: Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it. article_number: '9' article_processing_charge: No author: - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 citation: ama: Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009 apa: Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009 chicago: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009. ieee: B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019. ista: Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9. mla: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009. short: B. Corominas-Murtra, Life 9 (2019). date_created: 2019-02-10T22:59:15Z date_published: 2019-01-15T00:00:00Z date_updated: 2023-08-24T14:43:41Z day: '15' ddc: - '570' department: - _id: EdHa doi: 10.3390/life9010009 external_id: isi: - '000464125500001' file: - access_level: open_access checksum: 7d2322cd96ace41959909b66702d5cf4 content_type: application/pdf creator: dernst date_created: 2019-02-11T10:45:27Z date_updated: 2020-07-14T12:47:13Z file_id: '5951' file_name: 2019_Life_Corominas.pdf file_size: 963454 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Life publication_identifier: eissn: - '20751729' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Thermodynamics of duplication thresholds in synthetic protocell systems tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '6029' abstract: - lang: eng text: Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy. article_number: '655' article_processing_charge: No author: - first_name: Marco full_name: Lindner, Marco last_name: Lindner - first_name: Aliz full_name: Tresztenyak, Aliz last_name: Tresztenyak - first_name: Gergö full_name: Fülöp, Gergö last_name: Fülöp - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - first_name: Adrian full_name: Prinz, Adrian last_name: Prinz - first_name: Iris full_name: Prinz, Iris last_name: Prinz - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Gerhard J. full_name: Schütz, Gerhard J. last_name: Schütz - first_name: Eva full_name: Sevcsik, Eva last_name: Sevcsik citation: ama: Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6. doi:10.3389/fchem.2018.00655 apa: Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655 chicago: Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655. ieee: M. Lindner et al., “A fast and simple contact printing approach to generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers Media S.A., 2019. ista: Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655. mla: Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers Media S.A., 2019, doi:10.3389/fchem.2018.00655. short: M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019). date_created: 2019-02-17T22:59:24Z date_published: 2019-01-24T00:00:00Z date_updated: 2023-08-24T14:45:38Z day: '24' ddc: - '540' department: - _id: JoDa doi: 10.3389/fchem.2018.00655 external_id: isi: - '000456718000001' file: - access_level: open_access checksum: 7841301d7c53b56ef873791b4b6f7b24 content_type: application/pdf creator: dernst date_created: 2019-02-18T15:10:34Z date_updated: 2020-07-14T12:47:17Z file_id: '6039' file_name: 2019_frontiers_Lindner.pdf file_size: 1766820 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Frontiers in Chemistry publication_identifier: eissn: - '22962646' publication_status: published publisher: Frontiers Media S.A. quality_controlled: '1' scopus_import: '1' status: public title: A fast and simple contact printing approach to generate 2D protein nanopatterns tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 6 year: '2019' ... --- _id: '6028' abstract: - lang: eng text: We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small. article_processing_charge: Yes (via OA deal) author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Martin full_name: Hairer, Martin last_name: Hairer citation: ama: Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816 apa: Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816 chicago: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816. ieee: M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019. ista: Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005. mla: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816. short: M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005. date_created: 2019-02-17T22:59:24Z date_published: 2019-02-08T00:00:00Z date_updated: 2023-08-24T14:44:31Z day: '08' ddc: - '500' department: - _id: JaMa doi: 10.1002/cpa.21816 external_id: isi: - '000475465000003' file: - access_level: open_access checksum: 09aec427eb48c0f96a1cce9ff53f013b content_type: application/pdf creator: kschuh date_created: 2020-01-07T13:25:55Z date_updated: 2020-07-14T12:47:17Z file_id: '7237' file_name: 2019_Wiley_Gerencser.pdf file_size: 381350 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 72' isi: 1 issue: '9' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1983-2005 publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: A solution theory for quasilinear singular SPDEs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 72 year: '2019' ... --- _id: '5945' abstract: - lang: eng text: In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy. article_processing_charge: No article_type: original author: - first_name: Mariela D. full_name: Petkova, Mariela D. last_name: Petkova - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Eric F. full_name: Wieschaus, Eric F. last_name: Wieschaus - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor citation: ama: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007 apa: Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.01.007 chicago: Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007. ieee: M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019. ista: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15. mla: Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007. short: M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15. date_created: 2019-02-10T22:59:16Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:42:47Z day: '07' department: - _id: GaTk doi: 10.1016/j.cell.2019.01.007 external_id: isi: - '000457969200015' pmid: - '30712870' intvolume: ' 176' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2019.01.007 month: '02' oa: 1 oa_version: Published Version page: 844-855.e15 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Cell publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/ scopus_import: '1' status: public title: Optimal decoding of cellular identities in a genetic network type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 176 year: '2019' ... --- _id: '5943' abstract: - lang: eng text: The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour. article_processing_charge: No article_type: original author: - first_name: Lukasz full_name: Klotz, Lukasz id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87 last_name: Klotz orcid: 0000-0003-1740-7635 - first_name: Konrad full_name: Gumowski, Konrad last_name: Gumowski - first_name: José Eduardo full_name: Wesfreid, José Eduardo last_name: Wesfreid citation: ama: Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406. doi:10.1017/jfm.2018.974 apa: Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2018.974 chicago: Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974. ieee: L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863. Cambridge University Press, pp. 386–406, 2019. ista: Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406. mla: Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:10.1017/jfm.2018.974. short: L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406. date_created: 2019-02-10T22:59:15Z date_published: 2019-03-25T00:00:00Z date_updated: 2023-08-24T14:43:13Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2018.974 ec_funded: 1 external_id: arxiv: - '1902.07931' isi: - '000526029100016' intvolume: ' 863' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07931 month: '03' oa: 1 oa_version: Preprint page: 386-406 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Experiments on a jet in a crossflow in the low-velocity-ratio regime type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 863 year: '2019' ... --- _id: '6042' abstract: - lang: eng text: Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques. alternative_title: - LNCS article_processing_charge: No author: - first_name: Maria full_name: Christakis, Maria last_name: Christakis - first_name: Matthias full_name: Heizmann, Matthias last_name: Heizmann - first_name: Muhammad Numair full_name: Mansur, Muhammad Numair last_name: Mansur - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Valentin full_name: Wüstholz, Valentin last_name: Wüstholz citation: ama: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13' apa: 'Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-17462-0_13' chicago: Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17462-0_13. ieee: M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Prague, Czech Republic, 2019, vol. 11427, pp. 226–243. ista: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.' mla: Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13. short: M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243. conference: end_date: 2019-04-11 location: Prague, Czech Republic name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2019-04-06 date_created: 2019-02-18T16:44:06Z date_published: 2019-04-04T00:00:00Z date_updated: 2023-08-24T14:47:45Z day: '04' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-17462-0_13 ec_funded: 1 external_id: isi: - '000681166500013' file: - access_level: open_access checksum: 9998496f6fe202c0a19124b4209154c6 content_type: application/pdf creator: dernst date_created: 2019-05-10T14:16:05Z date_updated: 2020-07-14T12:47:17Z file_id: '6408' file_name: 2019_LNCS_Christakis.pdf file_size: 773083 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 11427' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 226-243 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: '25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Semantic fault localization and suspiciousness ranking tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11427 year: '2019' ... --- _id: '6035' abstract: - lang: eng text: 'We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.' article_processing_charge: No author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Kostiantyn full_name: Potomkin, Kostiantyn last_name: Potomkin - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804' apa: 'Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804' chicago: 'Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.' ieee: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44.' ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control vol. 22, 39–44.' mla: 'Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.' short: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.' conference: end_date: 2019-04-18 location: Montreal, QC, Canada name: 'HSCC: Hybrid Systems Computation and Control' start_date: 2019-04-16 date_created: 2019-02-18T14:43:28Z date_published: 2019-04-16T00:00:00Z date_updated: 2023-08-24T14:47:21Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1145/3302504.3311804 ec_funded: 1 external_id: arxiv: - '1901.10736' isi: - '000516713900005' file: - access_level: open_access checksum: 28ed56439aea5991c3122d4730fd828f content_type: application/pdf creator: cschilli date_created: 2019-03-05T09:27:18Z date_updated: 2020-07-14T12:47:17Z file_id: '6067' file_name: hscc19.pdf file_size: 3784414 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 22' isi: 1 keyword: - reachability analysis - hybrid systems - lazy computation language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 39-44 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 'Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control' publication_identifier: isbn: - '9781450362825' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: 'JuliaReach: A toolbox for set-based reachability' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2019' ...